Variant report

Variant	rs1250087
Chromosome Location	chr4:1248287-1248288
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1248223-1248310	HUVEC	blood vessel:	n/a	n/a
2	SETDB1	chr4:1248048-1249404	U2OS	brain:	n/a	n/a
3	POLR2A	chr4:1248224-1248327	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:1247960-1248575	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
2	chr4:1236808..1249320-chr4:1336333..1343819,66	MCF-7	breast:
3	chr4:1242091..1248517-chr4:1279714..1285424,16	MCF-7	breast:
4	chr4:1235141..1249133-chr4:1336906..1347308,118	MCF-7	breast:
5	chr4:1238004..1248980-chr4:1275065..1286840,30	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C4orf42-1	chr4:1246779-1248377	ENSG00000196810.4
2	lnc-C4orf42-1	chr4:1244047-1249698	ENSG00000196810.4

No data

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000090316	Chromatin interaction
ENSG00000163945	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10013662	1.00[MEX][hapmap]
rs11932075	0.88[YRI][hapmap]
rs11932230	1.00[EUR][1000 genomes]
rs1250104	0.87[ASW][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs1250127	1.00[EUR][1000 genomes]
rs1272043	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1481168	1.00[MEX][hapmap]
rs1680077	1.00[EUR][1000 genomes]
rs2127909	1.00[EUR][1000 genomes]
rs28750743	1.00[MEX][hapmap]
rs4246689	1.00[EUR][1000 genomes]
rs4974567	1.00[TSI][hapmap]
rs4974626	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4974635	1.00[EUR][1000 genomes]
rs4974645	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs57106389	1.00[EUR][1000 genomes]
rs58168130	1.00[EUR][1000 genomes]
rs61053739	1.00[EUR][1000 genomes]
rs6818213	1.00[MEX][hapmap]
rs6835204	1.00[MEX][hapmap]
rs6836809	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6836952	1.00[EUR][1000 genomes]
rs7659524	1.00[EUR][1000 genomes]
rs7676912	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs900023	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs900031	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
6	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
10	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
11	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
12	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
13	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
15	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
16	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
17	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
19	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
20	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
21	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
22	esv1811773	chr4:1228251-1287474	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
23	esv1800629	chr4:1228451-1287274	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
24	esv1812851	chr4:1228451-1287274	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
25	esv1823612	chr4:1228451-1287274	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
26	esv1825633	chr4:1228451-1287274	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
27	esv1838677	chr4:1231540-1274734	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
28	nsv878334	chr4:1232910-1254930	Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
29	esv1839490	chr4:1237014-1254930	Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
30	nsv878335	chr4:1237014-1254930	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
31	nsv878336	chr4:1238859-1254930	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
32	nsv878337	chr4:1240091-1254930	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
33	esv1837491	chr4:1241969-1259650	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
34	nsv593298	chr4:1244267-1342521	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1244200-1248400	ZNF genes & repeats	Fetal Muscle Leg	muscle
2	chr4:1244200-1249200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr4:1244200-1249400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr4:1244200-1249800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:1244400-1249000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:1244600-1249200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr4:1244800-1250400	Weak transcription	Psoas Muscle	Psoas
8	chr4:1245000-1249000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:1245400-1258400	Weak transcription	Ovary	ovary
10	chr4:1245400-1282400	Weak transcription	Brain Angular Gyrus	brain
11	chr4:1245600-1248600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:1245600-1266800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:1245800-1249400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr4:1245800-1261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:1245800-1278600	Weak transcription	Gastric	stomach
16	chr4:1245800-1282600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:1245800-1282600	Weak transcription	Right Ventricle	heart
18	chr4:1246000-1282600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:1246200-1248400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:1246400-1248600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr4:1246400-1248800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:1246400-1249600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:1246600-1249600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:1246800-1249200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr4:1247000-1248600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:1247000-1249400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr4:1247000-1256000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:1247400-1248600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:1247400-1254000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:1247400-1254200	Weak transcription	Spleen	Spleen
31	chr4:1247400-1263000	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:1247800-1248400	Weak transcription	Brain Anterior Caudate	brain
33	chr4:1247800-1249000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:1247800-1254600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:1247800-1258800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:1248000-1249600	Weak transcription	Esophagus	oesophagus
37	chr4:1248200-1250000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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